The Pokémon Trainer is the first playable Pokémon representative in the Super Smash Bros. series who is not an actual Pokémon. Though a selectable character, he is not an actual fighter, instead commanding any of his three Pokémon in the background of the stage, his team consisting of Squirtle, Ivysaur, and Charizard. The only move the trainer performs is Pokémon Change, which allows the player to switch out his three Pokémon at will throughout the battle. He also automatically switches Pokémon whenever one is KO'd. The Pokémon also run on a stamina system that weakens them, as their stamina decreases the longer they are out on the field. Their Final Smash is Triple Finish, which has the trainer send out all three Pokémon at once to attack.

In the Subspace Emissary, he allies with Lucas who helps him find his Charizard and Ivysaur. The two also encounter Wario and a large Subspace Army robot, Galleom. They are saved from the robot's detonation by Meta Knight, and they team with him, Marth and Ike afterwards. When encountering a huge Subspace Army group on the foothills of a mountain (Meta Knight has left to retake the Halberd), they are saved by Mario and his team (Link, Yoshi, Pit, and Kirby).

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Pokémon Change is the Pokémon Trainer's down special move, and by extension the down special move of Charizard, Squirtle, and Ivysaur. The move is based on the ability for players to switch out their Pokémon mid-battle in the Pokémon series, allowing players to switch between using Squirtle, Ivysaur, and Charizard in that order. Pokémon Change is also automatically used whenever one of the Pokémon's stamina is depleted or whenever one is KO'd. This move cannot be used immediately after respawning, or at all in midair. Status effects are also not carried over between Pokémon, though damage percentages are, and a Pokémon's stamina recharges while it is not in use.

Triple Finish is the Pokémon Trainer's Final Smash. The trainer sends out all three of his Pokémon to attack at the same time. Ivysaur hits with SolarBeam, a narrow beam of light that fires across the screen; Charizard with Fire Blast, a flame projectile that travels across the screen; and Squirtle with Hydro Pump, a water attack that sprays in multiple directions at close range, all of which deal continuous damage before opponents are knocked back by the final Fire Blast. If a player is too close to the team while they are attacking, they are knocked into the air rather than into the attack.

Throughout the entire attack, a text box designed after the ones in Pokémon Diamond and Pearl appears on the bottom of the screen, saying, "Take that, Triple Finish!" If the attack hits, the dialogue changes to say, "It's super effective!", referencing the type effectiveness mechanic of the Pokémon series.

A person who raises Pokémon and trains them as partners in battle. In battle, a Trainer gives orders to the Pokémon and uses items. It's not an exaggeration to say battles can be won or lost on a Trainer's single strategic move. Trainers pour their hearts into their Pokémon and share anger, sadness, and joy as they adventure in hopes of becoming Pokémon Masters.

Colonel: Right, and this Pokémon Trainer is controlling Squirtle, Ivysaur, and Charizard. They represent water, grass, and fire, and they're all powerful.

Snake: So he makes his Pokémon fight while he sits back and watches. Sounds like a good deal if you ask me.

Colonel: It's not like that, Snake. Those Pokémon wouldn't know what to do if the Pokémon Trainer wasn't there giving orders. In every battle, there's a soldier doing the fighting, and a commander telling him what to do. By working together as a team, they accomplish much more than either could on their own. So let's do this together, partner.

NA:Pop quiz! What do Misty, Brock, Cynthia, Iris, and Ash all have in common? That's right - they're all Pokémon Trainers! This Pokémon Master in the making is the same. Back in Super Smash Bros. Brawl, he fought to be the very best; like no one ever was. To smash them was his real test; to launch them was his cause!

PAL:Quiz time! What do Misty, Brock, Cynthia, Iris and Ash all have in common? That's right - they're all Pokémon Trainers! This Pokémon Master in the making is just the same. He fought to be the very best; like no one ever was - back in Super Smash Bros. Brawl. To smash them was his real test; to launch them was his cause.